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Chip type: Axiom_GW_Hu_SNP

The Axiom Genotyping Solution

Affymetrix' press release: Affymetrix The Axiom Genotyping Solution Expands Content, Throughput, and Customizable Arrays on a Single Platform, Oct 14, 2009.

From the press release: "The Axiom Solution will support both whole-genome association and candidate gene association studies with a level of customization not currently available. Researchers will no longer be constrained by the content of fixed-panel arrays. The complete genotyping platform employs enzyme-mediated, single-base sequencing steps for specificity in conjunction with affordable, reproducible, and highly automated workflows. [...] With a single platform and as few as one-and-a-half full-time technicians, a laboratory can process more than 750 samples per week with unmatched, minimal user intervention. The first commercial products from this offering will support genome-wide association studies and are expected to be delivered to customers this month." More at

> cdf <- AffymetrixCdfFile$byChipType("Axiom_GW_Hu_SNP", tags="r2")
> cdf

Path: annotationData/chipTypes/Axiom_GW_Hu_SNP
Filename: Axiom_GW_Hu_SNP,r2.cdf
Filesize: 185.23MB
Chip type: Axiom_GW_Hu_SNP,r2
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1190x1190
Number of cells: 1416100
Number of units: 575100
Cells per unit: 2.46
Number of QC units: 4

> unitNames <- getUnitNames(cdf)
> seqToHumanReadable(grep("^AFFX-", unitNames))
[1] "1-8004"
> seqToHumanReadable(grep("^AX-", unitNames))
[1] "8005-575100"

NOTE: There are no analysis methods in aroma.affymetrix that supports this chip type. There are several reasons for this, one is that the CEL files the Axiom platform are so called multi-channel CEL, and none of the preprocessing methods are prepared for this.